This is a revised PPG application to build a better understanding of T cell mechanisms in autoimmunity that has stemmed from the discovery of critical regulators of both T effector and T regulatory cells. We have discovered that IL-27 and the transcription factor aryl hydrocarbon receptor (AhR) play central roles in immune responses in animals and humans and these pathways impinge on all aspects of immune function, both adaptive and innate and include Tregs, Th17 cells and dendritic cells. Little is known about these new pathways, which appear crucial in CNS inflammation and have direct relevance to diseases such as multiple sclerosis. The primary goal of this program project grant (PPG) is to identify molecular mechanisms of how IL-27 inhibits effector T cells and induces regulatory Tr1 cells with a focus on two transcription factors cMaf and AhR, both of which are induced by IL-27 in responding Tr1 cells. The investigation of the inter-relationship of cytokines and transcription factors in both animal models and MS patients will allow a better basic understanding of immune abnormalities in MS and allow both the development of more specific immunomodulatory therapy and a mechanistic understanding of current therapies being used to treat MS. IFN, a widely used first line therapy in MS has been shown to act in part by the induction of IL-27, underscoring the importance of studying this pathway in CNS autoimmunity. This PPG brings together four investigators, each with unique strengths and expertise to investigate this new area. Project 1: (Kuchroo) Transcriptional regulation of effector and regulatory T cells in EAE; Project 2: (Littman) Transcriptional network analysis of Tr1 cells. Project 3: (Quintana) Role of AhR in the control of the innate immune response during the development of EAE. and Project 4: (Weiner) Role of IL-27 and AhR in the regulation of human effector and regulatory T cells in healthy subjects and MS patients. The revised PPG will establish a Multi-tiered Expression Analysis Core consisting of two components: Project 2 will undertake expression analysis using RNA-seq and ChlP-seq technologies and Core B will undertake multiplex expression analysis using the latest digital Nanostring technology to analyze the expression of transcripts in subsets and rare populations. The core will service all projects. An Administrative Core will coordinate the various administrative aspects of the PPG and a Scientific Advisory Board has been assembled to provide scientific oversight.